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Hmmm, is it more seaweedy, or like an eggy sulphur smell? I find seaweedy smells tend to come with more algae, and eggy smells with lots of decaying organics - both could be happening here! Almost certainly IMO it's just that disturbing the submerse plant roots has also disturbed the waste...

Shouldn't be a problem, especially after 2 years. I would keep as many floating plants as you can and don't remove all the floating ones your removing at once though, just to avoid any temporary water quality fluctuations from suddenly removing 70% plant mass. Removing submerse growth is always...

I've kinda suspected this for a while now, the "moss balls" we buy for aquariums do look a bit different (longer/courser algal strands) and less uniform than pictures of examples collected from nature. I guess true Marimo algae needs colder water with less competition from other algae and plant...

Looks great, really like a sunken section of botanical garden :).